Molecular aspects of Omicron, vaccine development, and recombinant strain XE: A review

Abstract

The global pandemic of COVID-19 began in December 2019 and is still continuing. The past 2 years have seen the emergence of several variants that were more vicious than each other. The emergence of Omicron (B.1.1.529) proved to be a huge epidemiological concern as the rate of infection of this particular strain was enormous. The strain was identified in South Africa on November 24, 2021 and was classified as a "Variant of Concern" on November 26, 2021. The Omicron variant possessed mutations in the key RBD region, the S region, thereby increasing the affinity of ACE2 for better transmission of the virus. Antibody resistance was found in this variant and it was able to reduce vaccine efficiency of vaccines. The need for a booster vaccine was brought forth due to the prevalence of the Omicron variant and, subsequently, this led to targeted research and development of variant-specific vaccines and booster dosage. This review discusses broadly the genomic characters and features of Omicron along with its specific mutations, evolution, antibody resistance, and evasion, utilization of CRISPR-Cas12a assay for Omicron detection, T-cell immunity elicited by vaccines against Omicron, and strategies to decrease Omicron infection along with COVID-19 and it also discusses on XE recombinant variant and on infectivity of BA.2 subvariant of Omicron.

Keywords: Omicron; recombinant variants; spike region; vaccine; variant of COVID-19.

Figure 1

The Spike protein structure of SARS‐CoV‐2 virus. The Spike protein comprises the following structures: (1) Signal peptide: Guides virus to its targeted membrane; (2) N‐terminal domain: Helps in the binding interface of the virus; (3) Receptor‐binding domain/C‐terminal domain (CTD): Interacts with host's ACE2, extensively targeted for Covid‐19 vaccine development; (4) Fusion peptide: Helps in penetrating targeted cell membrane through either TMPRSS2 pathway or endosome‐cathepsin L pathway; (5) Heptad repeat 1&2: Forms the six‐helical package that is crucial for entry of S2 subunit into the host cell and also for viral fusion; (6) Transmembrane domain: Contributes towards membrane fusion and stabilizes trimeric structure; (7) Cytoplasmic domain: Anchors the Spike protein inside the viral membrane.

Figure 2

Amino acid mutations present on the Spike region of Omicron. Each domain regions are indicated in different colors.

Figure 3

Shows the variable number of mutations present in Spike specific region in variants of SARS‐CoV‐2 virus

Figure 4

The map showing the emergence of VOCs, VUM, and VOI in different parts of the world. VOC, Variant of Concern; VOI, Variant of Interest; VUM, Variant under monitoring.